The Program for High-Cost Medicines of the Brazilian Health Ministry was set up to respond to the demand for high unit-cost medication or for medication used for chronic diseases that imply a high overall cost for treatment. To describe the epidemiological and demographic profiles of patients enrolled in the program, a probabilistic-deterministic connection was made between data in sections of the Health Ministry's databases (DATASUS), namely, the Outpatient Information System (APAC/SIA) and the Mortality Information System (SIM). The cohort formed by linking databases identified 611,419 individuals who began treatment between 2000 and 2004. The analyses were disaggregated by sex, region of residence, diagnoses and most widely used drugs.The construction of this historical cohort made possible a description of the epidemiological characteristics and drugs used by the program's users. The database generated can also provide analyses for specific diseases, with results that can contribute to evaluations of effectiveness and efficiency of clinical protocols, in order to better inform decision-makers regarding the planning and supplying of high-cost medication by the Brazilian Health Ministry.